Ligand profile

CHEMBL4289998

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0AES6 Formula C₂₅H₂₆F₃N₁₁OS
pchembl 8.05 ~8.9 nM
Mol. weight 585.62 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4289998
UniProt (similar protein)
P0AES6
pchembl
8.050 (~8.9 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 585.62 Da
LogP (Crippen) 3.89
H-bond donors 3
H-bond acceptors 10
TPSA 140.74 Ų
Rotatable bonds 6
Aromatic rings 4 / 6
Heavy atoms 41
Fraction sp³ C 0.40
Formula C₂₅H₂₆F₃N₁₁OS

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 140.7
  • −1 ≤ LogP ≤ 5 3.89
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 585.6
  • LogP ≤ 5 3.89
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 140.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cc(-c2nc(C(F)(F)F)cs2)c(-c2cc(-c3nnn[nH]3)cnc2N2C3CCC2CN(C)C3)cn1
InChI 
InChI=1S/C25H26F3N11OS/c1-3-29-24(40)33-20-7-17(23-32-19(12-41-23)25(26,27)28)18(9-30-20)16-6-13(21-34-36-37-35-21)8-31-22(16)39-14-4-5-15(39)11-38(2)10-14/h6-9,12,14-15H,3-5,10-11H2,1-2H3,(H2,29,30,33,40)(H,34,35,36,37)
InChIKey 
MBCOBCDFYMQNQZ-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF02518

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_00051.

PDB 88

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 99

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)